GEO DataSets

(Submitter supplied) Phosphate is a necessary macronutrient for basic biological processes, plant growth, and agriculture. Plants modulate their root system architecture and cellular processes to adapt to phosphate deprivation albeit with a growth penalty. Excess application of phosphate in the form of fertilizer can lead to eutrophication and has negative environmental impact. Moreover, phosphate mined from rock reserves is a finite and non-recyclable resource and its levels are nearing complete depletion. more...

Organism:

Solanum lycopersicum; Solanum pennellii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22467 GPL16345

32 Samples

Download data: CSV

(Submitter supplied) A systems-level study identifies inter-specific translational regulation as important in the elevated CO2 response in two Solanum species

Organism:

Solanum pennellii; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16345 GPL22467

512 Samples

Download data: CSV, TXT

(Submitter supplied) Climate change has increased the frequency and intensity of floods that impact global agricultural productivity. To better understand the response mechanisms and evolutionary history of gene family member regulation across angiosperm phyla, we studied the rapid submergence response of rice, the legume Medicago truncatula, and two Solanum species, domesticated tomato (S. lycopersicum cv. M82) and its dryland-adapted wild relative S. more...

Organism:

Oryza sativa Japonica Group; Solanum lycopersicum; Medicago truncatula; Solanum pennellii

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

8 related Platforms

231 Samples

Download data: BED, BW, TXT, XLSX

(Submitter supplied) We report the global wound-induced gene expression profile to compare the underlying transcriptional mechansims among S. lycopersicum, jasmonic acid–insensitive1 (jai1) and S. pennellii.

Organism:

Solanum pennellii; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19694 GPL24633 GPL22916

48 Samples

Download data: XLSX

(Submitter supplied) Transcriptomics study which main goal is to elucidate the programme of gene expression triggered by water stress in leaflets of the drought-tolerant wild-related tomato Solanum pennellii (acc. PE47) compared with domesticated tomato (S. lycopersicum, cv. P73). In this study we used S. lycopersicum (Sl) (cv. P73) and S. pennellii (Sp) (acc. PE47) species displaying remarkable divergences regarding drought tolerance, to investigate the physiological and molecular responses in leaves of plants grown without stress (control) and after four days of water withholding (water stress, WS), when plant water loss was significant but leaves did not show visual dehydration symptoms yet. more...

Organism:

Solanum lycopersicum; Solanum pennellii

Type:

Expression profiling by array

Platform:

GPL4741

12 Samples

Download data: CEL

(Submitter supplied) The goal of this study was to perform RNA-seq expression analysis on Solanum lycopersicum cv. M82 X S. pennellii introgression lines, deriving expression Quantitative Trait Loci which were analyzed together with pre-existing genomic and phenotypic data to define genes and regulatory pathways controlling tomato root development and observed natural variation. We completed the RNAseq expression profiling analysis and developed a tool to display this information graphically in collaboration with Nicholas Provart at the University of Toronto: http://bar.utoronto.ca/efp_tomato/cgi-bin/efpWeb.cgi?dataSource=ILs_Root_Tip_Brady_Lab To identify candidate genes and pathways we focussed on one root growth trait, root growth angle, and identified two statistically significant genomic regions within tomato root growth angle QTL containing two candidate genes that likely control the gravitropic setpoint angle (CDC73 and PAP27), both of which are conserved between Arabidopsis and tomato, and which we tested using transgenic lines of the Arabidopsis orthologs. more...

Organism:

Solanum pennellii; Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16345 GPL22468 GPL22467

305 Samples

Download data: TSV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Solanum lycopersicum; Solanum pimpinellifolium; Solanum lycopersicum x Solanum pennellii; Solanum pennellii

Type:

Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

8 related Platforms

39 Samples

Download data: TXT

(Submitter supplied) By using DNA methylation of introgression lines as a marker of past paramutation, we characterise in details the paramutation of the \textit{H06} locus in crosses between Solanum lycopersicum and a range of tomato relatives and cultivars. Paramutation of H06 depends on the timing of sRNA production and conforms to the RNA-directed model of paramutation. By scanning the methylomes of tomato introgression lines for shared regions of differential methylation, thousands of candidate regions for paramutation are identified. more...

Organism:

Solanum pennellii; Solanum pimpinellifolium; Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii

Type:

Non-coding RNA profiling by high throughput sequencing

6 related Platforms

31 Samples

Download data: TXT

(Submitter supplied) RNA-seq of seedlings of four tomato species Solanum habrochaites, Solanum lycopersicum, Solanum pimpinelliolium, and Solanum pennellii. An additional panel of samples include many tissues from Solanum lycopersicum and Solanum pennellii in two light conditions

Organism:

Solanum lycopersicum; Solanum pennellii; Solanum habrochaites; Solanum pimpinellifolium

Type:

Expression profiling by high throughput sequencing

4 related Platforms

52 Samples

Download data: TXT

(Submitter supplied) High throughput sequencing was used to investigate the production of small RNAs from cultivated tomato cultivar M82 and its wild relative Solanum pennellii. In order to understand the pattern of inheritance of the samll RNAs, interspecific hybrids (F1 and F2) along with series of introgressed lines comprising precise short genomic regions from S. pennellii in M82 background were used.

Organism:

Solanum lycopersicum; Solanum lycopersicum x Solanum pennellii; Solanum pennellii

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL10777 GPL10776 GPL9245

18 Samples

Download data: FASTA